scRNAseq of whole lung at 4 wk after infection. Four male mice per strain from two NCan strains (PWK/PhJ and CC024) and two canonical strains (C57BL/6 and CC011) were infected with H37Rv by low-dose aerosol. At 4 wk after infection, mice were euthanized, and lungs were processed to capture GEX by scRNAseq and stained with a panel of 198 oligo-tagged antibodies to capture surface protein expression. (A and B) (A) UMAP of 58,689 high-quality cells retrieved from whole lung and (B) dot plot depicting expression for key genes from each cluster. Size of the dot is indicative of the proportion of cells per cluster expressing each gene, and the color represents average expression level. (C) Proportion of major immune cell types. Statistical significance was assessed via Mann–Whitney U test with Benjamini–Hochberg correction (ns = not significant [P > 0.05]). (D–F) Overall, the dataset averaged (D) 5,138 cells per mouse with (E) 53,543 reads/cell and (F) 1,573 mRNA detected/cell. Significance assessed using the Mann–Whitney U test. All box-and-whisker plots depict bounds from the 25th to 75th percentile, median line, and whiskers extending from min to max with all points shown. NK, natural killer cell; DC, dendritic cell.